Changed name to commandName

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

@@ -17,7 +17,8 @@ object BiopetExecutable {
       nl.lumc.sasc.biopet.pipelines.sage.Sage,
       nl.lumc.sasc.biopet.pipelines.basty.Basty),
     "tool" -> List(
-      nl.lumc.sasc.biopet.core.apps.WipeReads)
+      nl.lumc.sasc.biopet.core.apps.WipeReads,
+      nl.lumc.sasc.biopet.core.apps.BiopetFlagstat)
   )
   
   /**
@@ -26,7 +27,7 @@ object BiopetExecutable {
   def main(args: Array[String]): Unit = {
 
     def toBulletedList(m: List[MainCommand], kind: String = "", bullet: String = "-") =
-      "Available %ss:\n  ".format(kind) + bullet + " " + m.map(x => x.name).sorted.mkString("\n  " + bullet + " ")
+      "Available %ss:\n  ".format(kind) + bullet + " " + m.map(x => x.commandName).sorted.mkString("\n  " + bullet + " ")
 
     def usage(module:String = null): String = {
       if (module != null) checkModule(module)
@@ -53,7 +54,7 @@ object BiopetExecutable {
     
     def getCommand(module:String, name:String) : MainCommand = {
       checkModule(module)
-      val command = modules(module).find(p => p.name.toLowerCase == name.toLowerCase)
+      val command = modules(module).find(p => p.commandName.toLowerCase == name.toLowerCase)
       if (command == None) {
         System.err.println(s"ERROR: command '$name' does not exist in module '$module'\n" + usage(module))
         System.exit(1)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core
 
 trait MainCommand {
 
-  lazy val name = this.getClass.getSimpleName
+  lazy val commandName = this.getClass.getSimpleName
     .split("\\$").last
 
   def main(args: Array[String])

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala

@@ -460,9 +460,9 @@ object WipeReads extends MainCommand {
 
   val usage: String =
     s"""
-      |Usage: java -jar BiopetFramework.jar tool $name [options] -I input -l regions -o output
+      |Usage: java -jar BiopetFramework.jar tool $commandName [options] -I input -l regions -o output
       |
-      |$name - Tool for reads removal from an indexed BAM file
+      |$commandName - Tool for reads removal from an indexed BAM file
       |
       |Positional arguments:
       |  -I,--inputBAM              Input BAM file, must be indexed with